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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACAATCATCAGACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataatcactcttcttttgtccatcccccttatttgtatttcccctagttgttatataactgaaaaattaaagatttttaaatgcttataatatctatgctctttactag

Basic information

species Oryza sativa
transcript LOC_Os12g03060.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03060.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G017941_T01 (Zea mays), 5'ss of exon 5
CTACAATCATCAGACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataatcactcttcttttgtccatcccccttatttgtatttcccctagttgttatataactgaaaaattaaagatttttaaatgcttataatatctatgctctttactag
||||||||||||||||| || ||||| ||||||| |||| || |||||| ||| |   ||||||||       | ||| ||        |   |   || ||| | | || |  ||     || ||||||||  || ||  | |||  |  ||| |||||  ||||||| | ||| ||
CTACAATCATCAGACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgta-----ggtaactgttgg------cgctcattttttttttctctctctcagacaccatttaactgaagcatcaa--actttccatggctcataatcactatgct-tgtaccag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29618674|gb|CB623686.1|CB623686
EST:     ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAG                         AACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
genomic: ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataa ... tctttactagAACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
EST: gi|86904894|gb|CI310687.1|CI310687
EST:     ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAG                         AACTCCTTTGCAAGCTCCGAG
genomic: ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataa ... tctttactagAACTCCTTTGCAAGCTCCGAG
EST: gi|33653554|gb|CF276168.1|CF276168
EST:     ACATTTCTAAAGAAAAGCAAGCTGATTCAGCTTTAGTAGACATGCTGAAG                         AACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
genomic: ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataa ... tctttactagAACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
EST: gi|58668824|gb|CK057510.1|CK057510
EST:     ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAG                         AACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
genomic: ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataa ... tctttactagAACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
EST: gi|29657293|gb|CB653568.1|CB653568
EST:     ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAG                         AACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
genomic: ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataa ... tctttactagAACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
EST: gi|66920771|gb|CX107619.1|CX107619
EST:     ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAG                         AACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
genomic: ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataa ... tctttactagAACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
EST: gi|88356178|gb|CI627626.1|CI627626
EST:     ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAG                         AACTCCTTTGCAAGCTCCGAG
genomic: ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataa ... tctttactagAACTCCTTTGCAAGCTCCGAG
EST: gi|25798686|gb|CA754647.1|CA754647
EST:     ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAG                         AACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
genomic: ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataa ... tctttactagAACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
EST: gi|27576657|gb|CA999351.1|CA999351
EST:     ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAG                         AACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
genomic: ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataa ... tctttactagAACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
EST: gi|29686826|gb|CB683101.1|CB683101
EST:     ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAG                         AACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
genomic: ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataa ... tctttactagAACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
EST: gi|58597158|gb|CK007686.1|CK007686
EST:     ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAG                         AACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG
genomic: ACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataa ... tctttactagAACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACAATCATCAGACATTTCTAAAGAAAAGCAAGCTGATTCAACTTTAGTAGACATGCTGAAGgtattcataatcactcttcttttgtccatcccccttatttgtatttcccctagttgttatataactgaaaaattaaagatttttaaatgcttataatatctatgctctttactag

- - - - - - - - - -  AAAGAA
- - - - - - - - - - - AAGAAA
- - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG